
General background knowledge

@book{lehninger,
	author="David L. Nelson and Michael M. Cox",
	title="Lehninger Principles of Biochemistry, 4th edition",
	publisher="W. H. Freeman and Company",
	year="2004",
}
@book{eidhammer,
	author="Ingvar Eidhammer and Kristian Flikka and Lennart Martens and Svein-Ole Mikalsen",
	title="Computational Methods for Mass Spectrometry Proteomics",
	publisher="John Wiley \& Sons Ltd",
	year="2004",
}
@book{eidhammer2,
	author="Ingvar Eidhammer and Inge Jonassen and William R. Taylor",
	title="Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis",
	publisher="John Wiley \& Sons Ltd",
	year="2004",
}
@online{probe,
	author="UiB",
	title="PROBE",
	year="2012",
	url={http://www.uib.no/rg/probe},
}
@unpublished{SRM,
	author="Ingvar Eidhammer and Harald Barsnes and Geir Egil Eide and Lennart Martens",
	title="Computational and Statistical Methods for Protein Quantification by Mass Spectrometry",
}
@book{Martin:2002,
	author="Robert C. Martin",
	title="Agile Software Development: principles, patterns, and practices",
	publisher="Prentice Hall",
	year="2002",
}
@article{Steen:2004,
	author="Hanno Steen and Matthias Mann",
	title="The {ABC}s {and XYZs} of peptide sequencing",
	journal="Nature reviews. Molecular cell biology",
	volume="5 (9)",
	pages="699-711",
	year=2004,
}
@book{webUsability,
	author="Jakob Nielsen and Hoa Loranger",
	title="Prioritizing Web Usability",
	publisher="New Riders Press",
	year="2006",
}
@manual{scrumGuide,
	author="Ken Schwaber and Jeff Sutherland",
	title="The Scrum Guide",
	month=oct,
	year="2011",
	note="\url{http://www.scrum.org/storage/scrumguides/Scrum_Guide.pdf}",
}
@article{humanGenome,
	author="International Human Genome Sequencing Consortium",
	title="Finishing the euchromatic sequence of the human genome",
	journal="Nature",
	volume="431",
	pages="931-945",
	year="2004",
}
@online{genomeNews,
	author="Kate Ruder and Edward R. Winstead",
	title="A quick guide to sequenced genomes",
	url={http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml},
	urldate={2012-05-28},
}
@online{jettyTomcat,
	author="Greg Wilkins",
	title="Jetty vs Tomcat: A comparative analysis",
	month=may,
	year="2008",
	url={http://www.slideshare.net/noriaki/jetty-vs-tomcat},
	urldate={2012-05-29},
}

LIMS

@article{limsArticle,
	author="Christine Piggee",
	title="{LIMS} and the art of {MS} proteomics",
	journal="Analytical Chemistry",
	volume="80 (13)",
	pages="4801-4806",
	year="2008",
}
@article{limsHowTo,
	author="George Avery and Charles McGee and Stan Falk",
	title="Implementing {LIMS}: A How-To Guide",
	journal="Analytical Chemistry",
	volume="72 (1)",
	pages="57A-62A",
	year="2000",
}
@article{proteios,
	author="Jari H{\"a}kkinen and Gregory Vincic and Olle M\aa{}nsson and Kristofer W\aa{}rell and Fredrik Levander ",
	title="The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data",
	journal="Journal of Proteome Research",
	volume="8 (6)",
	pages="3037-3043",
	year="2009",
}

Protein sequence databases

@article{Apweiler:2004,
	author="Rolf Apweiler and Amos Bairoch and Cathy Wu",
	title="Protein sequence databases",
	journal="Current Opinion in Chemical Biology",
	volume="8",
	pages="76-80",
	year="2004",
}
@article{Bairoch:2000,
	author="Amos Bairoch and Rolf Apweiler",
	title="The {SWISS}-{PROT} protein sequence database and its supplement {T}r{EMBL} in 2000",
	journal="Nucleic Acids Research",
	volume="28, No.1",
	pages="45-48",
	year="2000",
}
@article{Butler:2002,
	author="Declan Butler",
	title="NIH pledges cash for global protein database",
	journal="Nature",
	volume="419",
	pages="101",
	year="2002",
}
@online{uniProtAbout,
	author="UniProt",
	title="About {U}ni{P}rot",
	month=mar,
	year={2012},
	url={http://www.uniprot.org/help/about},
	urldate={2012-03-21},
}
@online{blastVsSmith,
	author="Gustav Wieds",
	title="Bioinformatics explained: {BLAST} versus {S}mith-{W}aterman",
	url={http://www.clcbio.com/index.php?id=1098},
	urldate={2012-03-21},
}
@article{Altschul:1990,
	author="Stephen Altschul and Warren Gish and Webb Miller and Eugene Myers and David Lipman",
	title="Basic Local Alignment Search Tool",
	journal="Jornal of Molecular Biology",
	volume="215 (3)",
	pages="403-410",
	year="1990"
}

The UniProtJAPI

@online{uniProtJapi,
	author="{European Bioinformatics Institute}",
	title="{U}ni{P}rot{JAPI}",
	month=mar,
	year={2012},
	url={http://www.ebi.ac.uk/uniprot/remotingAPI/},
	urldate={2012-03-25},
}

Google Web Toolkit

@online{gwt,
      author="Google",
      title="{G}oogle {W}eb {T}oolkit {O}verview",
      month=mar,
      year={2012},
      url={http://code.google.com/webtoolkit/overview.html},
	urldate={2012-03-23},
}
@online{gwtServer,
      author="Google",
      title="{GWT}: {C}ommunicate with a {S}erver",
      month=mar,
      year={2012},
      url={http://code.google.com/webtoolkit/doc/latest/DevGuideServer Communication.html},
	urldate={2012-03-23},
}

HTML5 and Flex/Flash

@book{Pilgrim:2010,
	author="Mark Pilgrim",
	title="HTML5: Up and running",
	publisher="O'Reilly Media, Inc",
	year="2010",
}
@online{adobeFlex,
	author="Adobe",
	title="Flex",
	month=mar,
	year={2012},
	url={http://www.adobe.com/products/flex.html},
	urldate={2012-03-24},
}
@online{adobeFlashVsHtml,
	author="Danny Winokur",
	title="Flash to Focus on PC Browsing and Mobile Apps; Adobe to More Aggressively Contribute to HTML5",
	month=nov,
	year={2011},
	url={http://blogs.adobe.com/conversations/2011/11/flash-focus.html},
	urldate={2012-03-24},
}
@online{html5Diff,
	author="{World Wide Web Consortium}",
	title="{HTML}5 differences from {HTML}4",
	month=mar,
	year={2012},
	url={http://www.w3.org/TR/html5-diff/},
	urldate={2012-03-23},
}
@online{html4Spec,
	author="{World Wide Web Consortium}",
	title="{HTML} 4.01 {S}pecification",
	month=dec,
	year={1999},
	url={http://www.w3.org/TR/html401/},
	urldate={2012-03-23},
}
@online{w3cDOM,
	author="Philippe Le H\'{e}garet",
	title="Document Object Model (DOM)",
	month=jan,
	year={2005},
	url={http://www.w3.org/DOM/},
	urldate={2012-03-23},
}

Play Framework

@online{playIntro,
	author="{Play Framework}",
	title="{I}ntroducing {P}lay 2.0",
	month=mar,
	year={2012},
	url={http://www.playframework.org/documentation/2.0/Philosophy},
	urldate={2012-03-25},
}

Vaadin

@book{learningVaadin,
	author = "Nicolas Fr{\"a}nkel",
	title = "Learning Vaadin",
	publisher = "Packt Publishing",
	year = "2011",
}
@book{bookOfVaadin,
	author="Marko Gr{\"o}nroos",
	title="Book of Vaadin: 4th Edition",
	publisher="Vaadin, Ltd.",
	year="2012",
}
@online{whatIsVaadin,
	author="Vaadin",
	title="Introduction to {V}aadin {D}evelopment",
	month=mar,
	year={2012},
	url={https://vaadin.com/learn},
	urldate={2012-03-25},
}
@online{vaadinDock,
	author="Vaadin",
	title="Vaadin Dock February 2012",
	month=feb,
	year="2012",
	url={https://vaadin.com/dock},
	urldate={2012-03-27},
}

Authentication
@online{HashingJava,
	author="Open Web Application Security Project",
	title="Hashing Java",
	month=may,
	year="2012",
	url={https://www.owasp.org/index.php/Hashing_Java},
	urldate={2012-05-25},
}
@book{appliedCrypto,
	author="Alfred J. Menezes and Paul C. van Oorschot and Scott A. Vanstone",
	title="Handbook of Applied Cryptography",
	publisher="CRC Press",
	year="1996",
}
@online{breakMD5,
	author="Xiaoyun Wang and Hongbo Yu",
	title="How to Break MD5 and Other Hash Functions",
	url={http://merlot.usc.edu/csac-f06/papers/Wang05a.pdf},
	urldate={2012-05-25},
}
@online{generalServerSecurity,
	author="National Institute of Standards and Technology",
	title="Guide to General Server Security",
	url={http://csrc.nist.gov/publications/nistpubs/800-123/SP800-123.pdf},
	month=jul,
	year="2008",
	urldate={2012-04-29},
}

